Key Laboratory of Marine Bio-resource Sustainable Utilization, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.
Gene. 2012 Feb 15;494(1):17-23. doi: 10.1016/j.gene.2011.12.002. Epub 2011 Dec 11.
The extreme variability of the mitochondrial (mito) genomes of bivalves makes it difficult to understand their evolutionary dynamics, given that species from different families do not share comparable features. We compared the mitogenomes from four Paphia clams (three of them were firstly sequenced) and found that mitogenome reorganization among the four congeneric species is not random but follows phylogenetic trends. Start/stop codon variations are species-correlated rather than gene-correlated, and bear useful phylogenetic information. Unique start/stop codon usage in P. euglypta and A+T content in P. amabilis indicates that these mitogenome-level characters, usually considered to be conservative features in other lineages, may not be phylogenetically evolved, but may have evolved via species-specific mitogenomic maintenance mechanisms. Variable divergence of two trnM genes in different lineages may demonstrate differences in mechanisms by which paralogous trnM genes are maintained. Sequence alignment analysis indicates that the VNTRs in the four mitogenomes have a common origin. The rationale of the subgenus Neotapes Kuroda and Habe, 1971 was supported by evidence from morphological characters, mitogenomic features, as well as phylogenetic analyses using cox1 and rrnS genes. The data suggest that the taxonomic basis of the subgenus should be "smooth surface" but not "undulated lines," and P. textile should be classified to the Neotapes subgenus.
双壳类动物的线粒体（mito）基因组具有极强的变异性，这使得人们难以理解其进化动态，因为不同科的物种并不具有可比的特征。我们比较了四种宝贝科蛤类（其中三种是首次测序的）的线粒体基因组，发现这四个同属物种的线粒体基因组重排并非随机发生，而是遵循系统发育趋势。起始/终止密码子的变化与物种相关，而与基因无关，具有有用的系统发育信息。P. euglypta 中独特的起始/终止密码子使用和 P. amabilis 中的 A+T 含量表明，这些线粒体水平的特征，通常被认为在其他谱系中是保守的，可能不是系统发育进化的，而是通过特定物种的线粒体基因组维持机制进化的。不同谱系中两个 trnM 基因的可变分化可能表明了同源 trnM 基因的维持机制存在差异。序列比对分析表明，四个线粒体基因组中的 VNTRs 具有共同的起源。形态特征、线粒体基因组特征以及cox1 和 rrnS 基因的系统发育分析都支持了 Kuroda 和 Habe 于 1971 年提出的 Neotapes 亚属的分类学依据。数据表明，该亚属的分类学基础应该是“光滑表面”而不是“起伏线”，而 P. textile 应该被归入 Neotapes 亚属。
